Hi - tx for (fast) reply. Ok ... with this result ...
(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1
/home/.galaxy/tooldeps/_conda/envs]$ trim_galore --version
-bash: trim_galore: command not found
Environment is:
(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1
/home/.galaxy/tooldeps/_conda/envs]$ env
XDG_SESSION_ID=45352
HOSTNAME=storage1.hpc
SELINUX_ROLE_REQUESTED=
TERM=xterm-256color
SHELL=/bin/bash
HISTSIZE=1000
SSH_CLIENT=10.55.40.3 55438 22
PERL5LIB=/root/perl5/lib/perl5:/usr/local/lib/perl5:
SELINUX_USE_CURRENT_RANGE=
QTDIR=/usr/lib64/qt-3.3
OLDPWD=/home/.galaxy/tooldeps/_conda/envs/__hisat2@2.1.0
QTINC=/usr/lib64/qt-3.3/include
PERL_MB_OPT=--install_base /root/perl5
SSH_TTY=/dev/pts/2
QT_GRAPHICSSYSTEM_CHECKED=1
USER=root
LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45:
MAIL=/var/spool/mail/root
PATH=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3/bin:/usr/lib64/qt-3.3/bin:/root/perl5/bin:/opt/pbs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/puppetlabs/bin:/root/bin
CONDA_PATH_BACKUP=/usr/lib64/qt-3.3/bin:/root/perl5/bin:/opt/pbs/default/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/opt/puppetlabs/bin:/root/bin
CONDA_PREFIX=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
CONDA=/home/.galaxy/tooldeps/_conda
PWD=/home/.galaxy/tooldeps/_conda/envs
LANG=en_ZA.UTF-8
MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles:/apps/etc/modulefiles
LOADEDMODULES=
KDEDIRS=/usr
PS1=(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3)
\[\e[1;31;40m\][\u@\h \w]$\[\e[0m\]
SELINUX_LEVEL_REQUESTED=
HISTCONTROL=ignoredups
SHLVL=1
HOME=/root
CONDA_PS1_BACKUP=\[\e[1;31;40m\][\u@\h \w]$\[\e[0m\]
PERL_LOCAL_LIB_ROOT=:/root/perl5
LOGNAME=root
QTLIB=/usr/lib64/qt-3.3/lib
SSH_CONNECTION=10.55.40.3 55438 10.55.40.1 22
MODULESHOME=/usr/share/Modules
CONDA_DEFAULT_ENV=/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
LESSOPEN=||/usr/bin/lesspipe.sh %s
XDG_RUNTIME_DIR=/run/user/0
QT_PLUGIN_PATH=/usr/lib64/kde4/plugins:/usr/lib/kde4/plugins
PERL_MM_OPT=INSTALL_BASE=/root/perl5
XAUTHORITY=/tmp/.Xauthority.root
BASH_FUNC_module()=() { eval `/usr/bin/modulecmd bash $*`
}
_=/usr/bin/env
(/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3) [root@storage1
/home/.galaxy/tooldeps/_conda/envs]$
------------------------------------------------------------------------
*From:* Björn Grüning <bjoern.gruen...@gmail.com>
*Sent:* 10 July 2018 08:38:15
*To:* Van Wageningen, GERHARD [gerha...@sun.ac.za];
galaxy-dev@lists.galaxyproject.org
*Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda
environment
Hi,
can you do:
. /home/.galaxy/tooldeps/_conda/bin/activate
'/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3
And see if you can execute trim_galore from the commandline and get the
help?
Ciao,
Bjoern
Am 10.07.2018 um 08:34 schrieb Van Wageningen, GERHARD [gerha...@sun.ac.za]:
Hi Bjoern, thanks for the pointer ... We are running the default
dependency_resolvers_conf.xml now and that, along with the symlinks hint
has helped with a lot of the tool dep. issues. But there is still a
pathing issue we are stuck on.
Take for example the trim_galore tool.
The error is
/home/.galaxy/database/jobs_directory/007/7480/tool_script.sh: line 25:
trim_galore: command not found
And the script is:
#!/bin/bash
# The following block can be used by the job system
# to ensure this script is runnable before actually attempting
# to run it.
if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
exit 42
fi
[ "$CONDA_DEFAULT_ENV" =
"/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3" ] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/.galaxy/tooldeps/_conda/bin/activate
'/home/.galaxy/tooldeps/_conda/envs/__trim-galore@0.4.3' >
conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; trim_galore --version >
/scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7477 2>&1; ln -s
'/home/.galaxy/database/files/013/dataset_13139.dat' input_1.fastq &&
trim_galore --phred33 --output_dir ./ input_1.fastq
--dont_gzip && if [ -f input_1_trimmed.fq.gz ] ; then mv
input_1_trimmed.fq.gz input_1_trimmed.fq ; fi && if [ -f
input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ;
fi && if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz
input_2_val_2.fq ; fi && if [ -f input_1_unpaired_1.fq.gz ] ; then mv
input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi && if [ -f
input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz
input_2_unpaired_2.fq ; fi
In fact most of the tools do this post-upgrade - where they cannot find
a file.
Here is the trace from hisat2 - it fails in a similar way so we conclude
that there is a common underlying fault here that is affecting the
pathing of the scripts.
Any ideas how we should go about finding this error?
Thanks, Gerhard
PS Here is the hisat2 output.
#!/bin/bash
# The following block can be used by the job system
# to ensure this script is runnable before actually attempting
# to run it.
if [ -n "$ABC_TEST_JOB_SCRIPT_INTEGRITY_XYZ" ]; then
exit 42
fi
[ "$CONDA_DEFAULT_ENV" =
"/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426"
] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/.galaxy/tooldeps/_conda/bin/activate
'/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426'
> conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; [ "$CONDA_DEFAULT_ENV" =
"/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426"
] ||
MAX_TRIES=3
COUNT=0
while [ $COUNT -lt $MAX_TRIES ]; do
. /home/.galaxy/tooldeps/_conda/bin/activate
'/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426'
> conda_activate.log 2>&1
if [ $? -eq 0 ];then
break
else
let COUNT=COUNT+1
if [ $COUNT -eq $MAX_TRIES ];then
echo "Failed to activate conda environment! Error was:"
cat conda_activate.log
exit 1
fi
sleep 10s
fi
done ; hisat2 --version >
/scratch2/galaxy/tmp/GALAXY_VERSION_STRING_7484 2>&1; set -o | grep -q
pipefail && set -o pipefail; ln -s
'/home/.galaxy/database/files/013/dataset_13248.dat' genome.fa &&
_hisat2-build_ -p ${GALAXY_SLOTS:-1} genome.fa genome && ln -f -s
'/home/.galaxy/database/files/013/dataset_13238.dat' input_f.fastq &&
ln -f -s '/home/.galaxy/database/files/013/dataset_13243.dat'
input_r.fastq && hisat2 -p ${GALAXY_SLOTS:-1} -x 'genome' -1
'input_f.fastq' -2 'input_r.fastq' |
samtools sort - -@ ${GALAXY_SLOTS:-1} -l 6 -o
'/home/.galaxy/database/jobs_directory/007/7484/galaxy_dataset_19227.dat'
The job fails when it cannot find “hisat2-build”.
Fatal error: Exit code 127 ()
/home/.galaxy/database/jobs_directory/007/7484/tool_script.sh: line 41:
hisat2-build: command not found
The PATH variable should be exported with installation
(/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/env.sh):
PATH=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43/bin:$PATH;
export PATH
HISAT2_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43;
export HISAT2_ROOT_DIR
HISAT_ROOT_DIR=/home/.galaxy/tooldeps/hisat/2.0.3/iuc/package_hisat_2_0_3/dc03603edd43;
export HISAT_ROOT_DIR
The conda environment with dependencies seems to be there:
/home/.galaxy/tooldeps/_conda/envs/mulled-v1-3b104c294f65450b09ba89d24826c61eddd553d789c9f1ae48a29715de1b7426/bin
Björn Grüning <bjoern.gruen...@gmail.com>;
galaxy-dev@lists.galaxyproject.org
------------------------------------------------------------------------
*From:* Björn Grüning <bjoern.gruen...@gmail.com>
*Sent:* 05 July 2018 22:00:58
*To:* Van Wageningen, GERHARD [gerha...@sun.ac.za];
galaxy-dev@lists.galaxyproject.org
*Subject:* Re: [galaxy-dev] Conda problems: Failed to activate conda
environment
Hi Gerhard,
it seems your tool is picking up the old tool_dependency version and not
the conda version of python.
Have a look at
https://github.com/galaxyproject/galaxy/blob/dev/config/dependency_resolvers_conf.xml.sample